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Pinus kwangtungensis is an endangered evergreen conifer tree species, and its in situ conservation has been considered one of the most critical issues. However, relative protection is limited by the lack of understanding of its community structure and underlying assembly processes. To study how the species diversity and assembly processes of Pinus kwangtungensis coniferous forest (CF) differed with regional climax community, this study established a series forest dynamic plots both in CF and evergreen deciduous broadleaved mixed forest (EDBM). By performing comparison analysis and PER-SIMPER approaches, we quantified the differences in species diversity and community assembly rules. The results showed that the species α-diversity of CF differed greatly from the EDBM both in species richness and evenness. In addition, the stochastic process acted a more important role in determining species composition, indicating the uncertainty in presence of species. The soil phosphorus and changeable calcium content were the main factors driving the differences in biodiversity, which the importance of soil nutrient factors in driving species composition. Our study highlighted that we should consider the community structure and ecological process when conducting conservation of Pinus kwangtungensis. [ABSTRACT FROM AUTHOR]

Relatively little attention has been paid to the underlying mechanisms determining the dominance of non-indigenous species (NIS) once established, despite being regarded as a proxy of invasion success and potential impacts in recipient communities. To bridge this knowledge gap, here we evaluate the potential direct and indirect effects of community filters on the dominance of two widespread NIS in the Baltic Sea: Marenzelleria spp. and the round goby (Neogobius melanostomus) within their corresponding communities. We applied a structural equation modelling approach to assess the direct and indirect effects amongst multiple abiotic and biotic variables on the relative biomass (as proxy of dominance) of NIS. The biotic variables represented the taxonomic- and functional diversity of the recipient communities, as well as the trait similarity between NIS and native species. We observed a comparable influence of abiotic and biotic drivers on the dominance of both NIS , with biotic variables having a somewhat stronger overall direct effect. Specifically, the dominance of both NIS was similarly affected negatively by the richness and positively by the evenness of the native communities. However, we also detected that both NIS might need different ecological strategies to become dominant in their recipient communities, which underwent similar assembly processes. Such strategies were partly highlighted by the different degrees of trait similarity between each NIS and their respective co-occurring native species. A better understanding of the underlying processes affecting NIS dominance is of high relevance to mitigate potential impacts of NIS once established. Furthermore, the provided approach could be further applied to unveil the potential strategies that NIS might follow in other regions and ecosystem types. [ABSTRACT FROM AUTHOR]

Pinus kwangtungensis is an endangered evergreen conifer tree species, and its in situ conservation has been considered one of the most critical issues. However, relative protection is limited by the lack of understanding of its community structure and underlying assembly processes. To study how the species diversity and assembly processes of Pinus kwangtungensis coniferous forest (CF) differed with regional climax community, this study established a series forest dynamic plots both in CF and evergreen deciduous broadleaved mixed forest (EDBM). By performing comparison analysis and PER-SIMPER approaches, we quantified the differences in species diversity and community assembly rules. The results showed that the species α-diversity of CF differed greatly from the EDBM both in species richness and evenness. In addition, the stochastic process acted a more important role in determining species composition, indicating the uncertainty in presence of species. The soil phosphorus and changeable calcium content were the main factors driving the differences in biodiversity, which the importance of soil nutrient factors in driving species composition. Our study highlighted that we should consider the community structure and ecological process when conducting conservation of Pinus kwangtungensis.

To preserve natural ecosystems and their biodiversity, there is a need to anticipate future ecosystem changes through better understanding of underlying drivers and assembly processes determining community composition. Assembly processes can be understood as a set of filters acting at different spatio‐temporal scales that jointly define the structure and composition of communities. Here, we explore the underlying assembly processes shaping marine fish species distribution and composition, using the heavily exploited North Sea. Our aims are to study 1) the relative importance of the different assembly processes shaping marine fish communities, 2) the key environmental drivers determining species distributions and composition, and to 3) quantify the role of traits in determining species niches and responses to the environment. Specifically, we fit a joint species distribution model (JSDM) using 31 years of standardized scientific bottom trawl survey data for 67 fish species. We use a set of environmental variables and species' traits representing morphology, life history, reproduction and diet, while also accounting for phylogenetic relationships of species. Environmental variables, primarily related to temperature, explained over one third of the variance in species occurrence, while spatial effects explained half of the variability across species. This shows that environmental filtering and spatially‐structured processes are the main drivers shaping the community assembly. Furthermore, among the total variance of individual species occurrences, 12.5% could be explained by traits, which improve the mechanistic understanding on species responses to environmental change. Hence, model predictions from JSDMs accounting for traits, environmental niches and potential interactions among multiple species can provide relevant simulations and forecasts with the potential to inform spatial management and conservation efforts aiming to preserve biodiversity and its associated services vital for human well‐being. [ABSTRACT FROM AUTHOR]

Rockfish (genus Sebastes) assemblages can inform mechanisms of coexistence and maintenance of diversity in ecological communities. Coexistence theory characterizes ecological assemblages as following either a deterministic niche differentiation model, or a stochastic lottery model. We used natural abundances of carbon and nitrogen stable isotopes from the tissues of ten co-occurring species of rockfish to assess position, size, and overlap of trophic niches in this diverse assemblage. We created a stochastic null model and compared observed values against the null model to determine if patterns were consistent with a deterministic or a stochastic model. We classified rockfish species as either demersal or pelagic. Mean δ13C and δ15N values differed among pelagic and demersal rockfish species and mean position was more variable than what was predicted by our null model. All species had relatively small trophic niches compared to occupied trophic niche space for the entire assemblage and trophic niche size was smaller than what was predicted by our null model. Trophic niche overlaps varied from 32% to 189% but were substantially lower than predicted by our null mode. All observed trophic niche metrics were different than the stochastic null model. This rockfish assemblage follows a deterministic model of community composition. [ABSTRACT FROM AUTHOR]

The diversity of species combinations observable in sampling units reflects a species' uneven distribution and preference for specific abiotic and biotic conditions – a phenomenon most commonly expressed in terms of ecological assembly rules of plant communities and other sessile organisms (e.g. subtidal algae, invertebrates and coral reefs). We present comspat, a new R package that uses grid or transect data sets to measure the number of realized (observed) species combinations (NRC) and the Shannon diversity of realized species combinations (compositional diversity; CD) as a function of spatial scale. NRC and CD represent two measures from a model family developed by Pál Juhász‐Nagy based on information theory. Classical Shannon diversity measures biodiversity based on the number and relative abundance of species, whereas the specific version of Shannon diversity presented here characterizes biodiversity and provides information on species coexistence relationships; both measures operate at fine‐scale within the sampling unit or within the community. comspat offers two commonly applied null models, complete spatial randomness and random shift, to disentangle the textural, intraspecific and interspecific effects on the observed spatial patterns. Combined, these models assist users in detecting and interpreting spatial associations and inferring assembly mechanisms. Our open‐sourced package provides a vignette that describes the method and reproduces the figures from this paper to help users contextualize and apply functions to their data. [ABSTRACT FROM AUTHOR]

'Brejos de altitude' is an ecosystem that has been subjected to severe exploitation, leading to an intense reduction in Brazil. Understanding the patterns of bryophyte diversity and composition, particularly of specialized species such as the epiphylls, to anthropic and abiotic variables is crucial for implementing protection measures.We investigated the relationship between composition and diversity of epiphyllous bryophytes and anthropic (edge effects) and abiotic (altitude) variables at local (within each 'Brejo') and regional (set of three 'Brejos') scale. Abiotic and anthropic variables were correlated with alpha and beta diversity (decomposed into species replacement and richness differences) using GLM. Their effects on species composition were evaluated using PERMANOVA.The localities at higher elevations harboured a richer bryoflora and overall beta diversity patterns were associated with altitude and locality, which acted over different scales. Regionally, the contribution of richness differences was limited with increasing altitude. Yet, dissimilarities among localities were associated with richness differences and replacement, denoting the importance of local factors. The composition was explained by local factors interacting with the regional altitudinal gradient. Anthropic activity was significant only when interacting with local factors and altitudinal gradient.Environmental filtering associated with altitude played a more important role in shaping the diversity and composition of epiphyllous bryophytes, at both regional and local scales. Each 'Brejo' acts as an ecological refuge, harbouring part of the whole environmental gradient, and presents a unique floristic composition. Moreover, partitioning beta diversity highlighted the interplay of local and regional forces shaping diversity patterns. [ABSTRACT FROM AUTHOR]

Deciphering the effect of neutral and deterministic processes on community assembly is critical to understand and predict diversity patterns. The information held in community trait distributions is commonly assumed as a signature of these processes, but empirical and modelling attempts have most often failed to untangle their confounding, sometimes opposing, impacts. Here, we simulated the assembly of trait distributions through stochastic (dispersal limitation) and/or deterministic scenarios (environmental filtering and niche differentiation). We characterized the shape of trait distributions using the skewness–kurtosis relationship. We identified commonalities in the co‐variation between the skewness and the kurtosis of trait distributions with a unique signature for each simulated assembly scenario. Our findings were robust to variation in the composition of regional species pools, dispersal limitation and environmental conditions. While ecological communities can exhibit a high degree of idiosyncrasy, identification of commonalities across multiple communities can help to unveil ecological assembly rules in real‐world ecosystems. [ABSTRACT FROM AUTHOR]

Pollinator‐mediated processes (biotic filtering, facilitation or competition) are often inferred by patterns of plant reproductive trait diversity (clustering or evenness of reproductive traits within the community). However, one single pattern can be generated by distinct processes, making difficult to predict the main process of community assembly. Incorporating fitness estimates should improve the link between pattern and process.We investigated patterns of flowering phenology and reproductive traits (floral colour, floral size and anther height) along the season of a pollinator‐depauperated and generalized community. We used data on fitness (pollen receipt and number of pollen tubes) to provide a functional link between trait patterns and assembly mechanisms. We also investigated whether the degree of co‐flowering depended on the floral abundance and pollination functional group (fly‐, bee‐, hummingbird‐pollinated and generalist species) of the plant species.High floral abundance in the flowering season was associated with low trait diversity in the community. Both features increased fitness at the community level. This indicates that similar species are benefited at periods of high floral abundance, probably due to the joint attraction of generalist pollinators in this pollinator‐depauperated community. In general, rare species flowered more synchronously with the community than abundant ones, although distinct patterns emerged depending on the floral trait and pollination functional group. Furthermore, species highly synchronous and possessing similar floral colour in relation to the community had higher fitness indicating that facilitative mechanisms act favouring flowering synchrony and trait similarity.Synthesis. Patterns of flowering synchrony and floral trait similarity indicate pollination facilitation in the studied community. Plants benefited from co‐flowering with species possessing similar floral colour via shared pollinator attraction. Thus, we empirically demonstrated some of the predictions of community assembly theory. [ABSTRACT FROM AUTHOR]

Mountains are interesting systems for studying patterns of diversity distribution and the role of environmental filters and competition on community assembly. According to the phylogenetic niche conservatism theory, the co-occurrence of closely related species might indicate that environmental filters are more important than competition when structuring communities in time and space. We investigated the patterns of phylogenetic diversity and the influence of environmental filters in the Brazilian rocky grasslands and tested the influence of phylogenetic niche conservatism. We placed 180 plots of 1 m2 in five sites along an altitudinal gradient at the Cipó Mountains (Espinhaço Range, southeastern Brazil) and surveyed all vascular plant species and edaphic variables. We assessed the phylogenetic diversity of the communities by calculating the phylogenetic species variability and phylogenetic species richness. These measures were related to altitude and the edaphic variables through a principal component analysis and regressions. Phylogenetic species variability decreased towards higher altitudes and less fertile sites, whereas phylogenetic species richness increased. Thus, the number of species and the degree of phylogenetic clustering increased with increasing altitude, suggesting that the intensity of abiotic factors acting as environmental filters increased with altitude and could be constraining species in the community to a smaller number of clades. [ABSTRACT FROM AUTHOR]

Abstract Environmental filters play an important role in plant community assembly. Evaluating spatial variation in functional traits across environmental gradients may help determine the environmental filters that play a role in community assembly and how plant communities respond to prevailing environmental conditions. In this study, we evaluated spatial variation in leaf traits (size, thickness, specific area and dry matter content) of coastal sand dune plant communities across 16 sites along a precipitation gradient in the Yucatan Peninsula. We described community-wide trait variation in terms of dispersion and dominant values across the gradient in order to answer the following questions: Which environmental filters explain variation in leaf traits? What ecological strategies, in terms of leaf economics, do these environmental filters favour? Mean specific leaf area and dispersion in leaf thickness tended to be lower in drier sites, suggesting that plants invest more biomass per leaf (a conservative strategy) and become more succulent as aridity increases. Contrary to expectation, leaf size increased with proximity to the coastline and dry matter content was significantly greater in the wettest region. Therefore, variation in these leaf traits content cannot be explained by the precipitation gradient. We have shown that predictable variation in some functional leaf traits can be found, even at small scales within the same vegetation zone in coastal sand dunes. Our study supports the notion that variation in water availability can be an important driver of functional trait distribution in the plant communities of some arid environments. Highlights • Leaf specific area tends to be lower in drier sites in coastal dunes of Yucatan. • Dispersion in leaf thickness in this ecosystem is also lower in drier sites. • Leaf size and dry matter content is variable, but unrelated to precipitation. • Precipitation patterns affect leaf trait distribution in coastal sand dunes. [ABSTRACT FROM AUTHOR]

Abstract Research on factors determining soil metacommunity patterns across multiple spatial scales is quite rare. In this study, we aimed to compare the mechanisms that drive species co-occurrence and consequently form the ground-dwelling macro-arthropod metacommunity structure at local (104 m) and regional (106 m) scales. For the comparison, we used three distant (approximately 200 km from each other) locations within the northeast black soil region of China. At each location, we had five sampling plots (at a distance of 500 m from each other), and at each plot, we had five sampling sites within agrolandscapes (10 m away from each other). At each site, we set three pitfall traps. Animals were collected three times: in May, July and September 2015. The analysis of the elements of metacommunity structure showed that the regional level of the metacommunity always demonstrated a Clementsian structure (a grouped distribution of species along environmental gradients), while the local scale metacommunity structure was dependent on sampling month and varied between Clementsian, random and nested distributions. Based on the results of a variance partitioning analysis, including pure environmental (environmental filtering) and pure spatial predictors (dispersal), as well as the interaction of environmental and spatial factors (shared fraction), we observed that the shared fraction at the regional scale was 30% larger than at the local scale. A species co-occurrence analysis further demonstrated that the observed C-scores were not significantly higher than simulated indices for each guild separately at the local scale. Our results suggest that biotic interactions are not the key drivers of metacommunity structure at the local scale in agriculture, while environmental filtering and dispersal appear to be key drivers of metacommunity structure at the regional scale. Highlights • Research on soil metacommunity patterns across multiple spatial scales is quite rare. • We aim to explore the drivers of metacommunity at local and regional scales. • Biotic interactions are not the key drivers of metacommunity structure at local scale. • Abiotic factors and dispersal to be the key drivers of structure at regional scale. [ABSTRACT FROM AUTHOR]

Trait‐based approaches and functional diversity have been previously used to enlighten our knowledge on the structure of community assemblages which are driven by species interactions or abiotic factors. We assess what amphibian functional diversity implies for the community assembly of amphibians of Europe and whether the use of different Functional Trait Groups (FTGs) affects the results. We used presence/absence atlas with 50 km × 50 km grain size and three functional diversity indices (FRic, RaoQ and FDiv) which reflect functional richness and divergence to estimate functional diversity patterns calculated for three FTGs: Morphological, Habitat‐related, Reproductive and the complete set of traits. To identify the two key processes (environmental filtering and limiting similarity) that may shape amphibian communities and how the relative importance of these processes could change using different FTGs, we used null models to test for non‐random patterns of functional diversity accounting or not for the difference in regional species pool. We show that for the same grid cell, for one FTG we might observe lower than randomly expected functional diversity (i.e., trait convergence or environmental filtering as the dominant community assembly process) while for another FTG or for the complete set of traits, higher than randomly expected functional diversity (i.e., trait divergence or limiting similarity as the dominant community assembly process). This highlights the role of trait selection on the inference drawn regarding community assembly. Furthermore, the number of traits (complete set vs. FTGs) used to quantify functional diversity also affects the conclusions regarding community assembly. We assess what amphibian functional diversity implies for the community assembly of amphibians of Europe and whether the use of different Functional Trait Groups (FTGs) affect the results. We show that for the same grid cell, for one FTG we might observe lower than randomly expected functional diversity (i.e. trait convergence or environmental filtering as the dominant community assembly process) while for another FTG or for the complete set of traits, higher than randomly expected functional diversity (i.e. trait divergence or limiting similarity as dominant community assembly process). [ABSTRACT FROM AUTHOR]

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The phylogenetic structure of communities (PSC) reveals how evolutionary history affects community assembly processes. However, there are important knowledge gaps on PSC patterns for annual communities and there is a need for studies along environmental gradients in dry ecosystems where several processes shape PSC. Here, we investigated the PSC of annual plants along an aridity gradient in Israel, including eight years, two spatial scales, the effects of shrubs on understory, and the phylogenetic signal of important traits. Increasing drought stress led to overdispersed PSC at the drier end of the gradient, indicating that species were less related than expected by chance. This was supported at a smaller spatial scale, where within the drier sites, communities in open - more arid - habitats were more overdispersed than those under nurse shrubs. Interestingly, some key traits related to drought resistance were not conserved in the phylogeny. Together, our findings suggested that while habitat filtering selected for drought resistance strategies, these strategies evolved independently along multiple contrasting evolutionary lineages. Our comprehensive PSC study provides strong evidence for the interacting effects of habitat filtering and plant-plant interactions, particularly highlighting that the conservative evolution of traits should not be assumed in future interpretations of PSC patterns. [ABSTRACT FROM AUTHOR]

Community disassembly is the non-random process of progressive species declines and losses. This process is usually studied to determine how various forces extirpate species, such as catastrophic disturbance, species invasions, habitat fragmentation, or unnatural/anthropogenic stressors. However, in ephemeral ecosystems, community disassembly is a natural and repeatable process. While many ephemeral ecosystems are aquatic (vernal pools, playa lakes, rock pools, saline lakes, phytotelmata, etc.), some disassembly patterns are applicable to other ecosystem types, including terrestrial ecosystems. As ephemeral waterbodies near the end of their hydroperiod, certain aspects fundamentally change. These fundamental changes or mechanisms cause visible patterns of community disassembly. Decreasing habitat size eliminates microhabitats and increases encounter rates between organisms, possibly increasing predation and competition. A harshening habitat eliminates low-tolerance species, changes the proportions of specialists/generalists, and forces organisms to acclimate, emigrate, or die. Additionally, ultraviolet light affects more of the water column, eliminating unprotected species. Furthermore, the entire metacommunity is often in similar stages of disassembly and collapses. Many of these mechanisms drive disassembly of terrestrial ephemeral habitats, such as animal carcasses, dung pads, or fungal fruiting bodies. Organisms obligate to ephemeral habitats have evolved to optimize their life history for a rapid life cycle with specific adaptations for themselves or their offspring to survive through the inactive period of the ecosystem. While some disassembly may occur too fast for biotic interactions or compensatory dynamics to be important, organisms undergoing natural disassembly should 'expect' it. Thus, predictions of disassembly based on internal or biotic patterns may be more common in natural disassembly scenarios than in human-induced disassembly of permanent ecosystems. Additionally, natural community disassembly should be more predictable and understandable than a permanent community's reaction to a never-before-seen anthropogenic disturbance. Community disassembly is an important ecological component of ephemeral ecosystems. The processes that occur during disassembly shape assemblages over ecologically and evolutionary relevant timescales. Understanding how natural disassembly can feed back to ultimately drive ecosystem structure and function increases our knowledge of fundamental ecology and provides for a new frontier of study. [ABSTRACT FROM AUTHOR]

Aim Plant species co-occur within communities in response to variation in environmental conditions, limited species dispersal and biotic interactions. We used surveys and resurveys of the same sites of three temperate forest plant communities to study patterns of association between co-occurring species pairs and to infer how these mechanisms contribute to community assembly. Our goal was to compare these forces among communities occupying more and less disturbed landscapes and examine how these have changed over the last 50 years. Location Wisconsin, USA. Methods We resurveyed 266 sites first surveyed in the 1950s to assess the patterns and dynamics of co-occurrence among understorey plant species in three community types. We then used checkerboard scores, null models and a newly developed framework to infer the mechanisms likely to have driven community assembly. Finally, we compared these across the three communities and two time periods. Results Species co-occur less often than expected in all three vegetation types and both periods. We detected high fractions of aggregated and segregated species pairs (up to 14% and 17%, respectively). In the fragmented southern upland forests and central sand plains, both biotic interactions and dispersal limitation may play important roles in community assembly with inferred dispersal limitation becoming more important since the 1950s. In the more continuous and intact northern upland forests, environmental filtering and biotic interactions appear to dominate community dynamics with little change over time. Aggregated and segregated species pairs made a similar contribution to our ability to infer these mechanisms. Main conclusions Environmental filtering, biotic interactions and dispersal limitation all appear to affect plant community structure in both time periods. However, the influence of dispersal limitation seems to be increasing in more fragmented forest landscapes, portending shifts in community composition and dynamics. Because aggregated and segregated species pairs may be shaped by similar processes both can be used to infer processes of community assembly. [ABSTRACT FROM AUTHOR]

Foundation species can change plant community structure by modulating important ecological processes such as community assembly, yet this topic is poorly understood. In alpine systems, cushion plants commonly act as foundation species by ameliorating local conditions. Here, we analyze diversity patterns of species' assembly within cushions and in adjacent surrounding open substrates (83 sites across five continents) calculating floristic dissimilarity between replicate plots, and using linear models to analyze relationships between microhabitats and species diversity. Floristic dissimilarity did not change across biogeographic regions, but was consistently lower in the cushions than in the open microhabitat. Cushion plants appear to enable recruitment of many relatively stress-intolerant species that otherwise would not establish in these communities, yet the niche space constructed by cushion plants supports a more homogeneous composition of species than the niche space beyond the cushion's influence. As a result, cushion plants support higher adiversity and a larger species pool, but harbor assemblies with lower β-diversity than open microhabitats. We conclude that habitats with and without dominant foundation species can strongly differ in the processes that drive species recruitment, and thus the relationship between local and regional species diversity. [ABSTRACT FROM AUTHOR]

Questions How similar or dissimilar must a species be to the resident plant community in order to successfully colonize grassland communities that vary in land-use intensity? Is land-use intensity an environmental filter that affects the survival rate of newcomers? Do species that are more likely to co-occur with the resident species show higher survival rates than those that are more similar/dissimilar to the resident community or randomly chosen species? Location Schwäbische Alb, Hainich and Schorfheide, Germany. Methods We planted different species from the regional grassland species pool into extant grassland communities exposed to different levels of land-use intensity. Species composition was recorded across 54 sites comprising meadows, mown meadows and grazed grasslands located within the 'Biodiversity Exploratories' project areas in three different regions of Germany. New species were selected for enrichment planting in the plots according to four different scenarios: species with highly similar or dissimilar traits, species with the highest degree of co-occurrence (derived from vegetation records held in the German vegetation reference database) and randomly chosen species. The changes in community mean trait distances brought about by enrichment planting and the transplant survival were related to land-use intensity. Results and Conclusion Land use was found to be an important environmental filter, as mean trait distance consistently declined with increasing land-use intensity across all scenarios. The planted species with the highest probability of co-occurrence with the resident species did not change the mean pair-wise trait distances across all plots, which indicates that they reflected the same degree of environmental filtering as the resident species. Accordingly, the species that commonly co-occur with the resident species survived best. These findings open a new avenue for using vegetation databases to assess the relative importance of environmental filtering. [ABSTRACT FROM AUTHOR]

Questions We investigated some commonly held assumptions of community assembly theory needed to provide accurate predictions of changes in plant species assemblages across environmental gradients or following environmental change. Do (1) dominant and subordinate species respond in the same way to changes in environmental variables; (2) plant species assemblages show higher interspecific than intraspecific trait responses; and (3) co-existing dominant species differ in their responses to the same environmental variables? Location Islands in Lakes Uddjaure and Hornavan, northern Sweden. Methods We explored the responses of forest understorey vegetation assemblages to variation in environmental resources across a chronosequence of 30 lake islands that differ in fire history, above-ground and below-ground resource availability and species diversity. For one plot on each island, we measured specific leaf area, leaf dry matter content and foliar N and P of all dominant and subordinate understorey plant species to assess species-specific and weighted and non-weighted community-level trait responses to variation across islands in all major local environmental drivers. Results Consistent with our expectations, we found that species responses to environmental conditions were not homogenous within assemblages, and that responses of dominant and subordinate species differed. Further, intraspecific variation was often an important component of local-scale plant community-level responses. Responses were often relatively consistent across species, but dominant species sometimes showed contrasting responses of the same trait to the same environmental factor. Finally, environmental factors that influenced community average trait values also affected functional diversity. Conclusions This study has shown that several common assumptions that underpin community assembly theory do not necessarily hold, and this can cause inaccuracies in predicting plant functional composition responses to changes in environmental variables. Because these assumptions are central to current models that predict vegetation responses to environmental change, it is crucial to further test in which particular environmental context and to what extent these assumptions are critical for model accuracy. [ABSTRACT FROM AUTHOR]

In 1859, Darwin had already identified environmental constraints and competition with the native community as major drivers of invasion success. Since then, a toolbox of indices and statistical approaches has been developed and commonly applied to test for the relative importance of these drivers. This toolbox is largely based on community ecology theory with the underlying hypothesis that patterns of trait (or phylogenetic) similarities between invaders and native species permit to disentangle the signatures of competition and environmental filtering. However, so far the performance of the indices and statistical approaches has not been thoroughly evaluated, and there exists no study exploring the sensitivity of the different methods given common biases in field data. This severely hampers intercomparisons of invasion studies and ultimately prevents the elaboration of general conclusions., In this study, we developed a mechanistic community assembly model to simulate invasion patterns across a range of communities and tested the performance of four different indices aiming at disentangling environmental filtering vs. competition from these patterns. Furthermore, we evaluated the sensitivity of the statistical methods to biases in the data (resulting from non-equilibrium dynamics or observation errors)., Our results indicated that the best performing index was mean distance to the native species (the average functional distance between the invader and all the species of the community), especially in heterogeneous landscapes. Further, we demonstrated that the detection of competition was more sensitive to the presence of biases in the data than the detection of environmental filtering., In conclusion, studying invasion mechanisms based on community patterns is possible when employing the appropriate statistical method, but it is highly sensitive to the quality of the data set used. [ABSTRACT FROM AUTHOR]

Aim The latitudinal gradient in species richness is one of the most studied biodiversity patterns. Here we explore a north-south gradient in earthworm diversity, and evaluate the importance of current and historical filters in shaping the distribution of present-day below-ground species richness. Location France. Methods Using high resolution data on earthworm distributions across France, we document the latitudinal gradients in alpha (α), beta (β) and gamma (γ) diversity. We relate these gradients to species' traits, taxonomic aggregation and co-occurrence patterns, and correlate them with the present climate and the history of glaciation in Europe. Results We found that γ-diversity decreases from south to north whereas α-diversity increases along the same latitudinal gradient. Communities in formerly glaciated regions are composed of smaller, more mobile species and show trait and taxonomical aggregation. In more southerly populations, which did not experience glaciation, earthworm species are larger, have smaller geographical ranges, and communities demonstrate a decrease in species co-occurrence resulting in lower local species richness. Main conclusions We show that species richness gradients can present different - sometimes opposite - latitudinal trends depending upon the scale of the analysis. This scale dependence sheds new light on the underlying causes of global biodiversity gradients. The opposing latitudinal trends of the different components of diversity suggest that recolonization following glaciations during the Pleistocene acted as an environmental filter, and that competitive exclusion may be a more dominant ecological force in these former refugial areas. Overall our results show that past climate changes have left a deep footprint on present-day earthworm diversity patterns, from community to macroecological scales, and that different mechanisms of earthworm community assembly may predominate at different latitudes. [ABSTRACT FROM AUTHOR]

Aim Investigations into how different facets of biodiversity are related has become a central research agenda in ecology. Here, we use a large-scale and high-resolution data set on bird distribution to examine the robustness of the relationships between species diversity and functional or phylogenetic diversity. Location France Methods We measured the functional and phylogenetic diversity of 1914 bird assemblages monitored over 10 years with a standardized protocol. We investigated the consequences of incorporating abundance versus presence-absence data, changing the number and identity of traits considered, or varying the spatial scale used to estimate functional and phylogenetic diversity. We further examined the outcomes of different null model procedures that aim to reveal ecological processes influencing the distribution of each facet of diversity. Results We found that the shape and strength of the relationship between species diversity and functional diversity are structured by several methodological choices. We show that increasing the quantity of information yielded by the indices (in particular, including abundances or increasing the number of traits considered) decreases the amount of functional redundancy estimated. Reducing the number of functional traits used to estimate functional diversity can change and even reverse the relationship of interest. Moreover, using alternative null models, we highlighted the specific role of environmental filtering and the link between species abundances and their functional originality (defined for a given species as the average of the functional distances with other species). The same tests applied to phylogenetic diversity revealed that its relationship with species diversity varies differently suggesting that this latter index cannot be used as a proxy for functional diversity. Main conclusions Our results show that the identification of patterns and processes linking species diversity to functional or phylogenetic diversity vary with methodological choices. We further show that the study of these sources of variation via robustness tests allows ecologically meaningful information to be separated from pure artefacts. [ABSTRACT FROM AUTHOR]

Understanding and disentangling different processes underlying the assembly and diversity of communities remains a key challenge in ecology. Species can assemble into communities either randomly or due to deterministic processes. Deterministic assembly leads to species being more similar (underdispersed) or more different (overdispersed) in certain traits than would be expected by chance. However, the relative importance of those processes is not well understood for many organisms, including terrestrial invertebrates. Based on knowledge of a broad range of species traits, we tested for the presence of trait underdispersion (indicating dispersal or environmental filtering) and trait overdispersion (indicating niche partitioning) and their relative importance in explaining land snail community composition on lake islands. The analysis of community assembly was performed using a functional diversity index (Rao's quadratic entropy) in combination with a null model approach. Regression analysis with the effect sizes of the assembly tests and environmental variables gave information on the strength of under- and overdispersion along environmental gradients. Additionally, we examined the link between community weighted mean trait values and environmental variables using a CWM- RDA. We found both trait underdispersion and trait overdispersion, but underdispersion (eight traits) was more frequently detected than overdispersion (two traits). Underdispersion was related to four environmental variables (tree cover, habitat diversity, productivity of ground vegetation, and location on an esker ridge). Our results show clear evidence for underdispersion in traits driven by environmental filtering, but no clear evidence for dispersal filtering. We did not find evidence for overdispersion of traits due to diet or body size, but overdispersion in shell shape may indicate niche differentiation between snail species driven by small-scale habitat heterogeneity. The use of species traits enabled us to identify key traits involved in snail community assembly and to detect the simultaneous occurrence of trait underdispersion and overdispersion. [ABSTRACT FROM AUTHOR]

Analysis of the phylogenetic similarity of co-occurring species at different spatial scales is increasingly used for decoding community assembly rules. Here, we integrated the analysis of phylobetadiversity and marked point pattern analysis to yield a new metric, the phylogenetic mark correlation function, kd( r), to quantify spatial phylogenetic structure of fully stem-mapped communities., kd( r) is defined as the expected phylogenetic distance of two heterospecifics separated by spatial distance r, and normalized with the expected phylogenetic distance of two heterospecifics taken randomly from a study area. It measures spatial phylogenetic turnover relative to spatial species turnover and is closely related with the spatially explicit Simpson index., We used simulated fully stem-mapped plant communities with known spatial phylogenetic structures to assess type I and II errors of the phylogenetic mark correlation function kd( r) under a null model of random phylogenetic spatial structure, and to test the ability of the kd( r) to detect scale-dependent signals of phylogenetic spatial structure. We also compared the performance of the kd( r) with two existing measures of phylobetadiversity that have been previously used to analyse fully stem-mapped plots. Finally, we explored the spatial phylogenetic structure of a 24-ha fully stem-mapped subtropical forest in China., Simulation tests showed that the new metric yielded correct type I and type II errors and accurately detected the spatial scales at which various processes (e.g. habitat filtering and competition) were invoked to generate spatial phylogenetic structures. The power of the kd( r) was not affected by a phylogenetic signal in species abundance and different topologies of the phylogenetic tree., Replacing phylogenetic distance by functional distance allows for application of the kd( r) to estimate spatial correlations in functional community structure. Thus, the kd( r) allows trait and phylogenetic structure to be analysed in the same framework. The phylogenetic mark correlation function is a powerful and accurate tool for revealing scale-dependent phylogenetic/functional footprints in community assemblages and allows ecologists to keep up with the increasingly available data of fully stem-mapped plots, functional traits and community phylogenies. [ABSTRACT FROM AUTHOR]

Theory has produced contrasting predictions related to flowering time overlap among coexisting plant species largely because of the diversity of potential influences on flowering time. In this study, we use a trait-based null modelling approach to test for evidence of deterministic assembly of species according to flowering time in an old-field plant community., Plant species coexisting in one-metre-square plots overlapped in flowering time significantly more than expected. This flowering synchrony was more pronounced when analyses focused on bee-pollinated species. Flowering synchrony was also observed for wind-pollinated species, although for only one of our two null model tests, highlighting the sensitivity of some results to different randomization methods. In general, these patterns suggest that relationships between pollinators and plants can influence community assembly processes., Because our study community is composed of approximately 43% native plant species and 57% exotic species, and because the arrival of new species may complicate plant-pollinator interactions, we tested whether flowering time overlap was altered by introduced species. Flowering synchrony was greater in plots with a higher proportion of introduced species. This pattern held for both null model tests, but was slightly stronger when analyses focused on bee-pollinated species. These results indicate that introduced species alter community flowering distributions and in so doing will inevitably affect pollinator-plant interactions., Finally, we tested whether our results were influenced by variation among study plots in above-ground biomass production, which some theory predicts will be related to the importance of competition. Our results were not influenced by this variation, suggesting that resource variation among our plots did not contribute to observed patterns., Synthesis: Our results provide support for predictions that coexisting species should display flowering synchrony, and provide no support for species coexistence via temporal niche partitioning at this scale in this study community. Our results also indicate that introduced species significantly alter the community assembly process such that flowering synchrony is more pronounced in plots with a greater proportion of introduced plant species. [ABSTRACT FROM AUTHOR]

Ecology Letters (2012) Abstract Although abiotic factors, together with dispersal and biotic interactions, are often suggested to explain the distribution of species and their abundances, species distribution models usually focus on abiotic factors only. We propose an integrative framework linking ecological theory, empirical data and statistical models to understand the distribution of species and their abundances together with the underlying community assembly dynamics. We illustrate our approach with 21 plant species in the French Alps. We show that a spatially nested modelling framework significantly improves the model's performance and that the spatial variations of species presence-absence and abundances are predominantly explained by different factors. We also show that incorporating abiotic, dispersal and biotic factors into the same model bring new insights to our understanding of community assembly. This approach, at the crossroads between community ecology and biogeography, is a promising avenue for a better understanding of species co-existence and biodiversity distribution. [ABSTRACT FROM AUTHOR]

Research has delivered convincing findings on the effect of biodiversity on ecosystem functioning and humankind. Indeed, ecosystems provide provisioning, regulating, supporting, and cultural services. The global value of annual ecosystem services of grasslands and rangelands is about US$ 232 ha year. Nevertheless, the precise evaluation of biodiversity benefits remains challenging. This issue is due to valuation methods, subjective assumptions, and complexity of drivers of plant community dynamics. Here, we review the primary factors that influence plant diversity of permanent grasslands, and we describe underlying processes. These factors must indeed be identified to focus policies meant to preserve and restore plant diversity and to advise farmers about efficient decision rules. We show that plant dynamics of permanent grasslands cannot be explained simply by agricultural management rules, e.g., grazing, fertilization, and mowing, implemented at the field scale. The configuration of the surrounding landscape, e.g., landscape heterogeneity, habitat fragmentation, and connectivity, acts as a species filter that defines the regional species pool and controls seed flow. The regional species pool often contains higher species richness in a heterogeneous landscape, because of a higher diversity of suitable habitats. This regional pool could be a major species sources for permanent grasslands according to the seed flow. We discuss the need to consider all of these factors to understand plant species composition of permanent grasslands and the necessity to study plant communities using both taxonomic and functional approaches. In order to report this integrative approach, we propose a conceptual model based on three ecological challenges-dispersal, establishment, and persistence-that are considered to act as filters on plant diversity, and a graphical representation of the complexity of such studies due to the interaction effects between plant dispersal abilities, forage productivity, disturbances induced by farming practices, and landscape heterogeneity on plant diversity. Last, we discuss the ability of farmers to manage each factor and the necessity of such study in the improvement of the current agro-environment schemes efficiency for farmland biodiversity restoration or preservation. [ABSTRACT FROM AUTHOR]

A fundamental question in community ecology is whether general assembly rules determine the structure of natural communities. Although many types of assembly rules have been described, including Diamond's assembly rules, constant body-size ratios, favoured states, and nestedness, few studies have tested multiple assembly rule models simultaneously. Therefore, little is known about the relative importance of potential underlying factors such as interspecific competition, inter-guild competition, selective extinction and habitat nestedness in structuring community composition. Here, we test the above four assembly rule models and examine the causal basis for the observed patterns using bird data collected on islands of an inundated lake. Thousand Island Lake, China. We collected data on presence-absence matrices, body size and functional groups for bird assemblages on 42 islands from 2007 to 2009. To test the above four assembly rule models, we used null model analyses to compare observed species co-occurrence patterns, body-size distributions and functional group distributions with randomly generated assemblages. To ensure that the results were not biased by the inclusion of species with extremely different ecologies, we conducted separate analyses for the entire assemblage and for various subset matrices classified according to foraging guilds. The bird assemblages did not support predictions by several competitively structured assembly rule models, including Diamond's assembly rules, constant body-size ratios, and favoured states. In contrast, bird assemblages were highly significantly nested and were apparently shaped by extinction processes mediated through area effects and habitat nestedness. The nestedness of bird assemblages was not a result of passive sampling or selective colonization. These results were very consistent, regardless of whether the entire assemblage or the subset matrices were analysed. Our results suggest that bird assemblages were shaped by extinction processes mediated through area effects and habitat nestedness, rather than by interspecific or inter-guild competition. From a conservation point of view, our results indicate that we should protect both the largest islands with the most species-rich communities and habitat-rich islands in order to maximize the number of species preserved. [ABSTRACT FROM AUTHOR]

A classic community assembly hypothesis is that all guilds must be represented before additional species from any given guild enter the community. We conceptually extend this hypothesis to continuous functional traits, refine the hypothesis with an eco-evolutionary model of interaction network community assembly, and compare the resultant continuous trait assembly rule to empirical data. Our extension of the “guild assembly rule” to continuous functional traits was rejected, in part, because the eco-evolutionary model predicted trait assembly to be characterized by the expansion of trait space and trait/species sorting within trait space. Hence, the guild rule may not be broadly applicable. A “revised” assembly rule did, however, emerge from the eco-evolutionary model: as communities assemble, the range in trait values will increase to a maximum and then remain relatively constant irrespective of further changes in species richness. This rule makes the corollary prediction that the trait range will, on average, be a saturating function of species richness. To determine if the assembly rule is at work in natural communities, we compared this corollary prediction to empirical data. Consistent with our assembly rule, trait “space” (broadly defined) commonly saturates with species richness. Our assembly rule may thus represent a general constraint placed on community assembly. In addition, taxonomic scale similarly influences the predicted and empirically observed relationship between trait “space” and richness. Empirical support for the model’s predictions suggests that studying continuous functional traits in the context of eco-evolutionary models is a powerful approach for elucidating general processes of community assembly. [ABSTRACT FROM AUTHOR]

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We extend the neutral theory of macroecology by deriving biodiversity models (relative species abundance and species-area relationships) in a local community-metacommunity system in which the local community is embedded within the metacommunity. We first demonstrate that the local species diversity patterns converge to that of the metacommunity as the size (scale) of the embedded local community increases. This result shows that in continuous landscapes no sharp boundaries dividing the communities at the two scales exist; they are an artificial distinction made by the current spatially implicit neutral theory. Second, we remove the artificial restriction that speciation cannot occur in a local community, even if the effects of local speciation are small. Third, we introduce stochasticity into the immigration rate, previously treated as constant, and demonstrate that local species diversity is a function not only of the mean but also of the variance in immigration rate. High variance in immigration rates reduces species diversity in local communities. Finally, we show that a simple relationship exists between the fundamental diversity parameter of neutral theory and Simpson's index for local communities. Derivation of this relationship extends recent work on diversity indices and provides a means of evaluating the effect of immigration on estimates of the fundamental diversity parameter derived from relative species abundance data on local communities. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, we investigate the trophic pyramid structure of 17 commonly studied ecosystems (terrestrial and varying aquatic environments). Food-web taxa from these ecosystems are classified into six functional groups: primary producers, herbivores, carnivores, omnivores, detritus, and detrital feeder; we find that the majority of the food webs exhibit an inverted pyramid structure with more higher trophic groups than lower ones. We find the average pyramid and inverted pyramid trophic distributions for these webs, and along with the uniform distribution, construct large-scale ecological networks based on these distributions. By creating and analyzing structural and flow matrices of these distributions using the cyber-ecosystem community assembly rule model, we compare the ecological parameters cycling, amplification, homogenization, indirect effects, and synergism. Excluding amplification, which does not occur in larger-scale models, we find that all network parameters show strong characteristic behaviors regardless of the trophic structure. Therefore, ecological network parameters are not considerably sensitive to different structures, indicating there may not be a preferred diet distribution. [Copyright &y& Elsevier]

With the advent of molecular phylogenies the assessment of community assembly processes has become a central topic in community ecology. These processes have focused almost exclusively on habitat filtering and competitive exclusion. Recent evidence, however, indicates that facilitation has been important in preserving biodiversity over evolutionary time, with recent lineages conserving the regeneration niches of older, distant lineages. Here we test whether, if facilitation among distant-related species has preserved the regeneration niche of plant lineages, this has increased the phylogenetic diversity of communities. By analyzing a large worldwide database of species, we showed that the regeneration niches were strongly conserved across evolutionary history. Likewise, a phylogenetic supertree of all species of three communities driven by facilitation showed that nurse species facilitated distantly related species and increased phylogenetic diversity. [ABSTRACT FROM AUTHOR]

A long-standing goal in evolutionary ecology is to determine whether the organization of communities is reflective of underlying deterministic processes. In this study, I examined patterns of species co-occurrence among eastern Plethodon salamanders and determined whether they were consistent with predictions from a guild model of competition-based community assembly. Using a database of 45 species and 4540 geographic sites, I found that patterns of co-occurrence were significantly nonrandom at both a regional and continental scale, and species of different size guilds were distributed more evenly in sites than was expected by chance. Sites with the highest species richness had consistent patterns of community composition, and with few exceptions, the same five species were present at all sites. Taken together, these results imply that larger Plethodon communities are assembled from simpler communities in a manner consistent with what is predicted through competitive mechanisms and suggest that stable species combinations are possible to achieve at various levels of species richness. These results also provide strong evidence consistent with the hypothesis that competitive-based community assembly is a general phenomenon in Plethodon and that interspecific competition is prevalent among the eastern species of this group. [ABSTRACT FROM AUTHOR]

1. Ecologists have long sought to derive assembly rules of ecological communities from the fundamental processes of population dynamics, but this goal has remained elusive. Neutral theory has reinvigorated the search by showing that patterns of relative species abundance closely resembling those actually observed arise under the assumption that, to a first approximation, all species are demographically identical on a per capita basis.2. Here a neutral model is proposed to incorporate all four fundamental processes of population dynamics: birth, death, immigration and emigration. This symmetric model demonstrates that patterns of relative species abundance are fully derivable from these basic processes of population dynamics.3. The theory derived extends the concept of community by showing that a continuum exists between large-scale (‘metacommunity’) and small-scale (‘local community’) processes, eliminating the artificial distinction between the two made by the current neutral theory and by the theory of island biogeography.4. The population-based species-abundance model describes very well the observed patterns of relative species abundance of tropical trees, breeding birds in the USA, aphids at Rothamsted, UK, and estuarine fishes in the north-east USA.5. The study also notes that while species assemblages may be well described by the neutral processes of population dynamics, the inference of mechanisms from pattern fitting is not warranted because one-to-one relationships between generating mechanisms and community patterns usually do not exist, either in the neutral realm or in the niche world.Functional Ecology(2005)19, 187–193 [ABSTRACT FROM AUTHOR]

The article discusses various reports published within the issue, including one by M. Claire Horner-Devine and colleagues on comparison of taxon co-occurrence patterns for macro- and microorganisms and another by Noah Fierer and colleagues on ecological classification of soil bacteria.